[gfmgfm]

Hello all,

Anyone has an idea how to count in tophat2 bam file the uniquely mapped reads?
Tophat(1) had mapping quality of 255 for uniquely mapping. Tophat2 has changed that, and I don't manage to figure out how to filter the bam file to get only the uniquely mapped reads.

Thanks.

[dpryan]

It's 50 now (at least the last time I looked). When in doubt:

samtools view accepted.bam | cut -f 5 | uniq | sort | uniq

to find out all of the MAPQs used by tophat (realistically, you could just take the first 1000 or so reads).

[gfmgfm]

Thanks a lot!